LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# 250 butane system for drude polarizability example (Langevin)

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
special_bonds lj/coul 0.0 0.0 0.5

pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4

read_data data.butane
  orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  4500 atoms
  scanning bonds ...
  5 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  9 = max dihedrals/atom
  reading bonds ...
  4250 bonds
  reading angles ...
  6000 angles
  reading dihedrals ...
  6750 dihedrals
  5 = max # of 1-2 neighbors
  8 = max # of 1-3 neighbors
  12 = max # of 1-4 neighbors
  17 = max # of special neighbors

comm_modify vel yes

group gBUTANE molecule 1:250
4500 atoms in group gBUTANE
group gCORES type 1 2 3
3500 atoms in group gCORES
group gDRUDES type 4 5
1000 atoms in group gDRUDES

pair_coeff    1    1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
pair_coeff    1    2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
pair_coeff    1    3 lj/cut/coul/long 0.044496 2.958040 # C3H H
pair_coeff    2    2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
pair_coeff    2    3 lj/cut/coul/long 0.044496 2.958040 # C2H H
pair_coeff    3    3 lj/cut/coul/long 0.029999 2.500000 # H H
pair_coeff    *  4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
pair_coeff    1    * thole 1.368000
pair_coeff    2    * thole 1.368000
pair_coeff    4    * thole 1.368000
pair_coeff    5    * thole 1.368000

neighbor 2.0 bin

variable vTEMP   equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS  equal 1.0

velocity gCORES  create ${vTEMP} 12345
velocity gCORES  create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345

fix fDRUDE all drude C C N D D

fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
  0 = # of size 2 clusters
  500 = # of size 3 clusters
  500 = # of size 4 clusters
  0 = # of frozen angles

fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
fix fNPH all nve

compute cTEMP all temp/drude

thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50

timestep 0.5
run 2000
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
  G vector (1/distance) = 0.367867
  grid = 36 36 36
  stencil order = 5
  estimated absolute RMS force accuracy = 0.031354
  estimated relative force accuracy = 9.44215e-05
  using double precision FFTs
  3d grid and FFT values/proc = 79507 46656
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 17
New max number of 1-2 to 1-4 neighbors: 17 (+0)
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10
  ghost atom cutoff = 10
  binsize = 5, bins = 8 8 8
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair lj/cut/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
  (2) pair thole, perpetual, skip from (1)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 26.29 | 26.29 | 26.29 Mbytes
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
       0            0    6535.5187      2714.74    248.45112    3820.7787    3724.3278    140.75328    1.4735401            0   -518.77975    595169.42   -594696.41    4439.7916    55742.797    334.61375    18.435655 
      50    1.8285224    3442.9216    2047.8425    187.41713    1395.0792    844.61103    802.43438    114.10967            0     -765.532    595242.44   -594842.98     3027.409    55742.797     200.4343    152.51723 
     100    3.7075663    2949.9137    1973.6229    180.62461    976.29073     358.0742    923.62856    174.43734            0   -919.88297    595306.76   -594866.72     2009.106    55742.797    229.49986     50.10998 
     150    5.5383921    2885.0697    1951.4547    178.59578    933.61499    234.26452    991.10197    194.44106            0   -910.03339    595293.22   -594869.38    4963.8801    55742.797    240.13548    14.311317 
     200    7.4217758     2890.343    1901.2801    174.00384    989.06297    227.57533    1077.5605    200.01467            0   -943.83325    595298.11   -594870.36    2977.5804    55742.797    237.27186    5.1150968 
     250    9.2994335     2922.348    1945.2702    178.02978    977.07781    212.26144    1127.8726    194.65284            0    -984.2934    595297.59   -594871.01    1592.2372    55742.797    243.81864    2.4147813 
     300    11.125204     2986.575     2013.159    184.24291    973.41608    212.85963    1130.6272    194.90599            0   -992.98724     595299.3   -594871.29    2816.8628    55742.797    252.63444     1.681279 
     350     12.99769    3051.4916    1978.4541    181.06675    1073.0375    228.43411    1195.4688    205.43169            0   -982.55178    595297.25      -594871    1408.7973    55742.797    248.34887    1.4666749 
     400    14.865399    3011.3983    1995.0047    182.58145    1016.3936    237.79955    1167.8185    197.49857            0   -1014.9362    595298.99   -594870.78    1456.5007    55742.797    250.45674    1.3981189 
     450    16.681866     3010.262    1976.9744    180.93133    1033.2876     216.3478    1196.7189    197.65964            0   -1005.6015    595298.72   -594870.56     1296.528    55742.797     248.1869    1.4022273 
     500    18.553431    3051.4554     2022.049    185.05652    1029.4064    220.84993    1196.1502    199.57249            0   -1014.3775    595298.27   -594871.05    2481.7571    55742.797    253.85835    1.3999256 
     550    20.416665    3086.0021    2018.9226     184.7704    1067.0796    221.95877    1215.9767     213.3405            0   -1012.5564    595299.48   -594871.12    1694.9376    55742.797    253.47686    1.3683935 
     600     22.27849    3110.9928    2030.8992    185.86649    1080.0935    220.35725    1253.9571    208.13083            0   -1030.4314    595298.96   -594870.88   -76.102661    55742.797    254.95682    1.4397403 
     650    24.087152     3154.373    2024.8469    185.31258    1129.5261    221.85968     1283.352    210.69451            0   -1015.2311    595299.67   -594870.82    1280.5683    55742.797    254.20302    1.4194509 
     700    25.941822      3133.85    2054.2045    187.99938    1079.6454    225.19338    1242.7819    192.54094            0   -1010.8971     595301.2   -594871.18     696.8538    55742.797     257.8878    1.4422435 
     750     27.79477    3189.0815    2103.7507    192.53381    1085.3308    219.46949    1243.7676    203.10695            0   -1010.2442    595299.93    -594870.7    483.46393    55742.797    264.14441    1.3796789 
     800     29.64589     3173.663    2053.4832    187.93336    1120.1799    219.59931    1256.2721    218.76191            0   -1003.0067    595299.37   -594870.81    543.09774    55742.797    257.81268    1.4005681 
     850     31.44585    3221.2873    2083.5215    190.68244    1137.7658     224.0492    1276.9143    219.91997            0    -1011.193    595298.47    -594870.4    143.54962    55742.797    261.60038    1.3772624 
     900    33.293605      3214.96    2053.8414    187.96614    1161.1187    222.21434    1296.0291    226.57612            0   -1013.6289    595300.61   -594870.68    473.39553    55742.797    257.85596    1.4053153 
     950    35.166863    3213.1086     2123.777     194.3666    1089.3317    221.79126    1251.6851    200.63798            0   -1014.0889    595300.01    -594870.7    1206.8497    55742.797    266.62111    1.4935247 
    1000    36.983663    3211.3103     2079.738    190.33618    1131.5723     225.4767    1260.2162    204.61245            0   -986.95685     595298.7   -594870.48    787.31501    55742.797     261.0928    1.4615275 
    1050    38.806926    3199.3221    2095.9148    191.81667    1103.4073    212.62976     1255.417    208.36886            0   -1001.9237    595299.13   -594870.21    239.45594    55742.797    263.14173    1.4246893 
    1100    40.634771    3199.8694    2067.6467     189.2296    1132.2227    235.50505    1264.2214    198.42446            0   -994.78564    595299.12   -594870.26    830.67515    55742.797    259.58627    1.4225726 
    1150    42.427903    3172.4663    2083.0988    190.64376    1089.3675    209.20043    1236.7213    204.50261            0   -990.26027    595299.43   -594870.22    1355.1408    55742.797    261.54264     1.389433 
    1200    44.302469    3178.2153    2055.1801    188.08866    1123.0351    230.76616    1258.2175    205.04893            0   -999.28826    595298.25   -594869.96     819.5423    55742.797    258.01926    1.4189827 
    1250    46.164956    3224.5367    2108.1449    192.93596    1116.3918    235.56939    1247.0387    212.74774            0   -1007.3896    595298.16   -594869.74   -146.38102    55742.797    264.67477    1.4395372 
    1300    48.015128    3286.0631    2125.3364    194.50931    1160.7267    236.69229    1272.7247    218.49151            0   -995.46842    595298.38    -594870.1    434.46496    55742.797    266.83295     1.451771 
    1350     49.79655    3247.1808    2087.4518    191.04214    1159.7291    215.07571     1301.219    211.43766            0   -995.15128    595297.24   -594870.09    1501.3496    55742.797    262.07016      1.44305 
    1400    51.624074    3194.7716    2041.9251    186.87557    1152.8466    236.94802    1261.0635    209.14663            0   -982.03995    595297.35   -594869.63    346.64925    55742.797    256.31352    1.5208162 
    1450    53.450535    3229.6083    2087.4545    191.04239    1142.1538    246.85361     1264.077    205.22437            0   -1003.5382    595299.44    -594869.9     278.1536    55742.797    262.08335    1.4087832 
    1500    55.288627    3249.6608    2089.8541      191.262    1159.8067    238.99337    1274.9502    206.61799            0   -988.99015    595297.98   -594869.75    636.34142    55742.797    262.36618    1.4595924 
    1550    57.093174    3273.2213    2122.5463    194.25397     1150.675    230.16428    1274.9965     195.7686            0   -979.24728    595298.84   -594869.85    528.01943    55742.797    266.47594    1.4678006 
    1600    58.978489    3288.6787    2120.7284     194.0876    1167.9503    229.10278    1274.2494    205.30619            0   -969.94195    595298.85   -594869.62    1126.6579    55742.797    266.23416    1.5026913 
    1650    60.803467    3286.3327    2148.1031    196.59291    1138.2295    234.18582    1256.2009    214.69184            0   -995.41699    595298.38   -594869.81   -457.07393    55742.797    269.67989    1.4977223 
    1700    62.624963    3296.9487    2092.8432    191.53556    1204.1055    238.05554    1313.8592    213.47968            0   -989.09874    595297.16   -594869.35    981.42569    55742.797     262.7423    1.4593707 
    1750     64.39829    3310.3958    2097.6547    191.97591    1212.7411    243.56621     1309.681    210.07115            0   -978.63733    595297.78   -594869.72   -41.877565    55742.797    263.31945    1.5344885 
    1800    66.216881    3229.7417    2079.7567    190.33789     1149.985    226.57585    1276.3941    202.60118            0   -984.26122    595298.62   -594869.94    515.97995    55742.797    261.07174    1.5239416 
    1850    68.038292    3199.6375    2033.1459     186.0721    1166.4916    242.84458    1267.7768    212.87764            0   -984.52187    595296.72   -594869.21    440.77319    55742.797    255.22287    1.4839954 
    1900    69.841965    3155.3872    2019.0731    184.78417    1136.3141    213.38104    1263.0105     213.0042            0   -980.43253    595296.92   -594869.57    469.76979    55742.797    253.48524    1.3965366 
    1950    71.702563    3191.9366    2051.5475    187.75621    1140.3891    211.61608    1278.9441     206.1048            0   -984.04544    595297.56   -594869.79    758.07165    55742.797    257.54478    1.4655839 
    2000    73.520102    3214.3938    2041.9357    186.87654    1172.4582    237.13198    1275.4194     218.0467            0   -985.25597    595296.76   -594869.64    375.81502    55742.797    256.33161    1.4761528 
Loop time of 73.5201 on 1 procs for 2000 steps with 4500 atoms

Performance: 1.175 ns/day, 20.422 hours/ns, 27.203 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 50.346     | 50.346     | 50.346     |   0.0 | 68.48
Bond    | 3.3227     | 3.3227     | 3.3227     |   0.0 |  4.52
Kspace  | 16.003     | 16.003     | 16.003     |   0.0 | 21.77
Neigh   | 1.3495     | 1.3495     | 1.3495     |   0.0 |  1.84
Comm    | 0.33013    | 0.33013    | 0.33013    |   0.0 |  0.45
Output  | 0.0044131  | 0.0044131  | 0.0044131  |   0.0 |  0.01
Modify  | 2.1068     | 2.1068     | 2.1068     |   0.0 |  2.87
Other   |            | 0.05755    |            |       |  0.08

Nlocal:    4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    8703 ave 8703 max 8703 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    860806 ave 860806 max 860806 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 860806
Ave neighs/atom = 191.29
Ave special neighs/atom = 13.3333
Neighbor list builds = 28
Dangerous builds = 0
Total wall time: 0:01:13
